Couple of differences I've noticed in 2on2 between SNES and Gens:
Framerate seems higher in SNES 2on2, as compared to SNES 5on5. I've noticed this on an actual SNES with my Super Everdrive as well.
You can speed burst out of control quickly by just spamming it. In Gens, you have to get checked really hard into the boards to lose control of your skater so that they can speed burst super fast.
Floater goals are very rare to come by.
Flying burrito saves don't work well at all, unless they're done across the goal line.
Penalty shots happen even with penalties off. Not sure how I feel about it, but I wish we could toggle it on / off.
Having a lot of fun with SNES 2on2 so far.